In TweetDeck I have several saved searches. This would cause a pop-up to come up constantly, so I turned off the alerts. However, there are some things I want to be alerted to. How can I enable alerts only for people that I'm following and disable alerts for my searches?
Click "Settings" (wrench in the upper right). In the settings dialog, click "Notifications", then click "Advanced Options for columns". That will make a bunch of checkboxes appear, which you can use to enable or disable the alerts on a column-by-column basis.